On 03/29/2012 11:02 AM, richard k belew wrote: > i'm trying to evaluate models generated by Modeller in comparison > to some built using threading methods (ITasser). GA341 seems the > primary coin-of-realm in Modeller-land
Maybe 5 years ago... the newer DOPE method is superior. See Protein Sci 17, 1881-1893, 2008 (#205 at http://salilab.org/publications/)
> but in trying to compare models, i'm finding Modeller > models that have excellent (> 0.8) GA341 scores but > pretty terrible (1 - 1.5) zDOPE scores. and so in comparison > to ITasser models with good zDOPE scores (~ -0.5), these > threaded models would seem preferred?
I would trust zDOPE over GA341. But neither zDOPE nor GA341 cares whether the model is generated by Modeller or by some other method - they simply take PDBs as input.
Ben Webb, Modeller Caretaker